Ion Research Panels:

Panel Name Research Area Genome Number of amplicons per pool
(# of tubes)
Tags Actions
Ion AmpliSeq™ BRCA1 and BRCA2 Panel
Cancer Research Human (hg19) Pool1: 55 amplicons
Pool2: 56 amplicons
Pool3: 56 amplicons
(3 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

BRCA1 and BRCA2 Results Files

BRCA1_2.YYYYMMDD.384WellPlateDataSheet.csv

This file contains all of the data for your 384 Well Plate. For each amplicon, you will find the pool information, its (row,column) coordinates, the AmpliconID, and the forward and reverse primers.

BRCA1_2.YYYYMMDD.concentration.tab

This file contains the concentration.

BRCA1_2.YYYYMMDD.designed.bed

Details the regions covered by the panel. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In.

BRCA1_2.YYYYMMDD.hotspotAnnot.csv

This file provides a list of the genes associated with each Fixed Panel, listed in cosmic id order and contains the following information: * Gene symbol * Accession id * COSMIC id * CDS Mutation - change occurred in the nucleotide sequence * AA Mutation - change occurred in the peptide sequence as a result of the mutation * Strand (+/-) * Coordinates (hg19) * Amplicon ID * Insert Sequence * Target URL – links to the COSMIC curated mutations database.

BRCA1_2.YYYYMMDD.hotspots.bed

The Hotspots BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels*. * Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.

BRCA1_2.YYYYMMDD.primerDataSheet.csv

This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).

BRCA1_2.YYYYMMDD.results_coverage_details.csv

This file contains the coverage details for the panel. This results file contains information about the Gene symbol, the Chromosome number and the start, end coordinates of each region covered, the number of amplicons required to cover that region, the number of bases that were covered, the number of targeted bases, the number of missed bases and the proportion of coverage.

BRCA1_2.YYYYMMDD.results_coverage_summary.csv

In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.

BRCA1_2.YYYYMMDD.submitted.bed

This file contains the regions that were submitted to AmpliSeq for design.

BRCA1_BRCA2.germline.lowstringency.pgm.3_6.YYYYMMDD.parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 3.6 for PGM runs

BRCA1_BRCA2.germline.lowstringency.pgm.4_0.YYYYMMDD.parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for PGM runs

plan.json

This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.

Data Analysis in the Torrent Browser

You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com. 1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab. 2) You will be asked to input your AmpliSeq.com login information: 3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel 4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete. 5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.

Summary: Mutations in tumor suppressor genes BRCA1 and BRCA2 have been implicated in hereditary breast and ovarian cancer. The Ion AmpliSeq™ BRCA1/2 Panel utilizes 167 amplicons to analyze the coding regions of both BRCA1 and BRCA2 genes.
Ion AmpliSeq™ Cancer Hotspot Panel v2
4475346
Cancer Research Human (hg19) Pool1: 207 amplicons
(1 tube)
DNA
Ready-to-Use Panel
FFPE
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

Select your Target Regions and Hotspot Regions BED files from the drop-down menus:

Variant Caller Plugin

* The designer currently only works for Human Reference Genome, hg19.

Summary: The Ion AmpliSeq™ Cancer Hotspot Panel v2 is a single pool of primers used to perform multiplex PCR for preparation of amplicon libraries from genomic "hot spot" regions that are frequently mutated in human cancer genes. This panel contains 207 amplicons in 1 pool.
Ion AmpliSeq™ Colon and Lung Research Panel v2
Cancer Research Human (hg19) Pool1: 92 amplicons
(1 tube)
DNA
Community Panel
Trial Kit Available
FFPE
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

Select your Target Regions and Hotspot Regions BED files from the drop-down menus:

Variant Caller Plugin

* The designer currently only works for Human Reference Genome, hg19.

Summary: The Ion AmpliSeq™ Colon and Lung Cancer Panel v2 is a single pool panel that analyses hotspot and targeted regions of 22 genes implicated in colon and lung cancers. This panel uses 92 amplicons for re-sequencing and analysis. (**Note: The trial kit version is not available for EMEA countries**)
Ion AmpliSeq™ Comprehensive Cancer Panel
4477685
Cancer Research Human (hg19) Pool1: 3996 amplicons
Pool2: 4008 amplicons
Pool3: 3991 amplicons
Pool4: 3997 amplicons
(4 tubes)
DNA
Ready-to-Use Panel
FFPE
Review panel Sign in to order

Cancer Panel Primer Pool Results Files

CCP.YYYYMMDD.designed.bed

Each row contains details about the regions covered by the panel: the chromosome number, the start and ending positions, the gene ID associated to the region and the pool ID in which the primers are placed. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In; the primer pool information is used by the Coverage Analysis plugin to display a plot of the average number of reads per amplicon per pool:

CCP.YYYYMMDD.hotspots.bed

The Hotspots BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels*. * Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.

CCP.YYYYMMDD.missed.bed

This file contains information about the regions that are missed by the design: the chromosome number and the (start,end) coordinates of the missed region.

CCP.YYYYMMDD.primerDataSheet.csv

This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).

CCP.YYYYMMDD.results_coverage_details.csv

This file contains the coverage details for the panel. This results file contains information about the Gene symbol, the Chromosome number and the start, end coordinates of each region covered, the number of amplicons required to cover that region, the number of bases that were covered, the number of targeted bases, the number of missed bases and the proportion of coverage.

CCP.YYYYMMDD.results_coverage_summary.csv

In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.

CCP.YYYYMMDD.submitted.bed

This file contains the regions that were submitted to AmpliSeq for design.

CCP_somatic_lowstringency_pgm_3.6_YYYYMMDD_parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 3.6 for PGM runs

CCP_somatic_lowstringency_pgm_4.0_YYYYMMDD_parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for PGM runs

CCP_somatic_lowstringency_p1_4.0_YYYYMMDD_parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for Proton runs

plan.json

This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.

Data Analysis in the Torrent Browser

You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com. The following example for the BRCA panel applies as well for the CCP panel. 1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab. 2) You will be asked to input your AmpliSeq.com login information: 3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel 4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete. 5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.

Summary: The Ion AmpliSeq™ Comprehensive Cancer Panel provides highly multiplexed target selection of genes implicated in cancer research. With all-exon coverage of 409 genes, this panel delivers fast, FFPE-compatible, target selection for a broad survey of key genes for semiconductor sequencing. The panel contains 15,992 amplicons in only 4 pools.
Ion AmpliSeq™ TP53 Panel
Cancer Research Human (hg19) Pool1: 12 amplicons
Pool2: 12 amplicons
(2 tubes)
DNA
Community Panel
Trial Kit Available
FFPE
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

Select your Target Regions and Hotspot Regions BED files from the drop-down menus:

Variant Caller Plugin

* The designer currently only works for Human Reference Genome, hg19.

Summary: The TP53 gene codes the tumor suppressor protein p53 which has been extensible researched in the field of Human Oncology. The Ion AmpliSeq™ TP53 Panel is a 2 pool panel with 24 amplicons designed to analyze all coding exons of the TP53 gene.
Ion AmpliSeq™ Colon and Lung Cancer Panel
Cancer Research Human (hg19) Pool1: 90 amplicons
(1 tube)
DNA
Community Panel
Review panel Sign in to order

Colon and Lung Panel Results Files

ColonLung.YYYYMMDD.384WellPlateDataSheet.csv

This file contains all of the data for your 384 Well Plate. For each amplicon, you will find the pool information, its (row,column) coordinates, the AmpliconID, and the forward and reverse primers.

ColonLung.YYYYMMDD.concentration.tab

This file contains the concentration (not sure if this is customer facing)

ColonLung.YYYYMMDD.designed.bed

Details the regions covered by the panel. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In.

ColonLung.YYYYMMDD.hotspotAnnot.csv

This file provides a list of the genes associated with each Fixed Panel, listed in cosmic id order and contains the following information:

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - change occurred in the nucleotide sequence
  • AA Mutation - change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon ID
  • Insert Sequence
  • Target URL – links to the COSMIC curated mutations database.

ColonLung.YYYYMMDD.hotspots.bed

The Hotspots BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels*.

* Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.

ColonLung.YYYYMMDD.primerDataSheet.csv

This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).

ColonLung.YYYYMMDD.results_coverage_summary.csv

In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.

ColonLung.YYYYMMDD.submitted.bed

This file contains the regions that were submitted to AmpliSeq for design.

colon.lung_somatic_lowstringency_pgm_3.6_YYYYMMDD_parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 3.6 for PGM runs

colon.lung_somatic_lowstringency_pgm_4.0_YYYYMMDD_parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for PGM runs

plan.json

This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.

Data Analysis in the Torrent Browser

You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com. The following example for the BRCA panel applies as well for the Colon and Lung panel.

1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab.

2) You will be asked to input your AmpliSeq.com login information:

3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel

4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.

5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.

Summary: The Ion AmpliSeq™ Colon and Lung Cancer Panel is a single pool panel that analyses hotspot and targeted regions of 22 genes implicated in colon and lung cancers. This panel uses 90 amplicons for re-sequencing and analysis.
Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel
Cancer Research Human (RefSeq) Pool 1: 85 amplicons
(1 tube)
RNA
Community Panel
Trial Kit Available
FFPE
Review panel Sign in to order

Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel Files

CSV file

The CSV file in this panel contains the assay names and references of the 61 unique gene fusions, 5 expression control genes, and 4 genes containing 5’ and 3’ imbalance assays. As indicated in the reference column, some EML4-ALK assays target fusions transcripts having updates to annotation in COSMIC v67 (denoted as COSFXXXX.1)

README

The README text file provides information about the panel design and analysis software solution.

Summary: Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel is designed to target a set of known fusion transcripts as well as expression imbalances between the 3’ and 5’ regions of the genes. The panel contains 85 amplicons in a single pool. (**Note: The trial kit version is not available for EMEA countries**)
Ion AmpliSeq™ AML Research Panel
Cancer Research Human (hg19) Pool1: 124 amplicons
Pool2: 113 amplicons
Pool3: 12 amplicons
Pool4: 15 amplicons
(4 tubes)
DNA
Community Panel
Standard
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite™ Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite™ Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

Select your Target Regions and Hotspot Regions BED files from the drop-down menus:

Variant Caller Plugin

* The designer currently only works for Human Reference Genome, hg19.

Summary: The Ion AmpliSeq™ AML Cancer Research Panel is a 4 pool panel utilizing 237 amplicons to analyze 19 genes implicated in acute myeloid leukemia.
Ion AmpliSeq™ Cancer Panel Primer Pool
4471262
Cancer Research Human (hg19) Pool1: 190 amplicons
(1 tube)
DNA
Ready-to-Use Panel
Review panel Sign in to order

Cancer Panel Primer Pool Results Files

CP.YYYYMMDD.designed.bed

Details the regions covered by the panel. This file is used for data analysis with the Torrent Browser / Variant Caller Plug-In.

CP.YYYYMMDD.hotspotAnnot.csv

This file provides a list of the genes associated with each Fixed Panel, listed in cosmic id order and contains the following information:

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - change occurred in the nucleotide sequence
  • AA Mutation - change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon ID
  • Insert Sequence
  • Target URL – links to the COSMIC curated mutations database.

CP.YYYYMMDD.hotspots.bed

The Hotspots BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels*.

* Note: To avoid the issue of ambiguous right alignment of indel calling, the Hotspots BED files are left aligned for optimal performance when used with Torrent Suite Variant Caller.

CP.YYYYMMDD.missed.bed

This file contains information about the regions that are missed by the design: the chromosome number and the (start,end) coordinates of the missed region.

CP.YYYYMMDD.primerDataSheet.csv

This file presents detailed information for the amplicons in the panel: a (sorted) amplicon ID number, the forward and reverse primers, the gene symbol, chromosome number and the (start,end) coordinates for the amplicon and for the insert (the amplicon without considering the primer length).

CP.YYYYMMDD.results_coverage_details.csv

This file contains the coverage details for the panel. This results file contains information about the Gene symbol, the Chromosome number and the start, end coordinates of each region covered, the number of amplicons required to cover that region, the number of bases that were covered, the number of targeted bases, the number of missed bases and the proportion of coverage.

CP.YYYYMMDD.results_coverage_summary.csv

In this file you will find for each gene, the chromosome number, the total number of amplicons, total number of bases submitted to design, the number of bases that were covered and the overall coverage (Covered bases/Total Bases). The number of exons in each entry point is available, as well as a distribution of the number of exons that were covered in proportion of 1, > 0.95, > 0.9, > 0.8, > 0.7, > 0.5, > 0.2, < 0.2 and at 0.

CP.YYYYMMDD.submitted.bed

This file contains the regions that were submitted to AmpliSeq for design.

CP_somatic_lowstringency_pgm_3.6_YYYYMMDD_parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 3.6 for PGM runs

CP_somatic_lowstringency_pgm_4.0_YYYYMMDD_parameters.json

JSON formatted file with optimized parameters to be manually uploaded for variant calling on TVC 4.0 for PGM runs

plan.json

This file contains all the information to automatically configure a run plan for this panel, when the panel's files are directly downloaded from the Torrent Server as shown below.

Data Analysis in the Torrent Browser

You can easily create a plan run on the Torrent Browser to analyze AmpliSeq panels by directly downloading them from your account at ampliseq.com. The following example for the BRCA panel applies as well for the CP panel.

1) Find and click the "AmpliSeq.com Import" link on the AmpliSeq section of the Plan tab.

2) You will be asked to input your AmpliSeq.com login information:

3) Select the appropriated panel; in this case we will select the BRCA1 and BRCA2 Panel

4) After clicking the "Import Selected" button a download screen displays the status of the download. Reload the page to verify the download is complete.

5) Once the download has finished, verify that the plan is available in the Ampliseq DNA Plans table: the plan is ready to be used.

Summary: The Ion AmpliSeq™ Cancer Panel Primer Pool is used to perform multiplex PCR for preparation of amplicon libraries from genomic "hot spot" regions that are frequently mutated in human cancer genes. This primer pool contains the same primers included in the Ion AmpliSeq™ Cancer Panel, but is now sold separately for use with the improved Ion AmpliSeq™ Library Kit 2.0. This panel contains 190 amplicons in 1 pool.
Ion AmpliSeq™ RNA Apoptosis Panel
4482571
Cancer Research Human (RefSeq) Pool 1: 267 amplicons
(1 tube)
RNA
Ready-to-Use Panel
Review panel Sign in to order

Apoptosis Ready-to-Use Design Details

The ready-to-use design details are available for download. In a compressed folder, there are a number of files with diverse information. Although the type of data in all of the files is plain text and they can be opened using any text editor, we recommend using a spreadsheet such as MS Excel for viewing their contents given their multicolumn format.

Apoptosis_Designed.bed

This file contains the RefSeq accession number of the RNA sequence (transcript) for which the primers were designed, the start and end coordinates of the amplicon relative to the transcript sequence, the amplicon ID and in the last column the HGNC gene symbol that is associated with the transcript identifier in the first column. The file contains one row for each gene or accession number submitted to design.

Note: the contents in this file are not viewable in the UCSC genome browser given that the RefSeq coordinates that it reports are not compatible with the browser.

Apoptosis_Primer.bed

This file provides similar but more detailed information than the file Apoptosis_Designed.bed . There are differences in the format of some columns and in the number of rows; the differences in format make this file compatible with the UCSC genome browser. This file presents two rows for each one of all of the targets submitted to design: one row for the forward primer and one row for the reverse primer. The start and end coordinates are for the position of the primer on the chromosome that is displayed in column 1. The second to last column reports the preferred TaqMan assay that can be used for verification. Also the gene symbol in the last column corresponds to the symbol submitted by the user (it might or might not be the HGNC symbol).

Apoptosis_DataSheet.csv

This file contains one row for each of the RefSeq accession numbers of the RNA sequences that are covered by the designed primers. For each row there is extensive information such as the names submitted by the user, the corresponding HGNC approved symbol, the amplicon ID, the sequence of the forward and reverse primers, the start and end coordinates of the primers relative to the RefSeq sequence, the coordinates of the start and end of the amplicon and the start and end of the insert sequence relative to their position in the chromosome and the strand of the chromosome in which the sequence is located.

Summary: The Ion AmpliSeq™ RNA Apoptosis Panel is a screening tool designed against 267 genes involved in the cellular apoptosis pathway. Included are genes associated with death receptor mediated apoptosis, cmyc, and p53 mediated apoptosis. This panel contains 267 amplicons in 1 pool.
Ion AmpliSeq™ RNA Cancer Panel
4482572
Cancer Research Human (RefSeq) Pool 1: 50 amplicons
(1 tube)
RNA
Ready-to-Use Panel
Review panel Sign in to order

Cancer50 Ready-to-Use Design Details

The ready-to-use design details are available for download. In a compressed folder, there are a number of files with diverse information. Although the type of data in all of the files is plain text and they can be opened using any text editor, we recommend using a spreadsheet such as MS Excel for viewing their contents given their multicolumn format.

Cancer50_Designed.bed

This file contains the RefSeq accession number of the RNA sequence (transcript) for which the primers were designed, the start and end coordinates of the amplicon relative to the transcript sequence, the amplicon ID and in the last column the HGNC gene symbol that is associated with the transcript identifier in the first column. The file contains one row for each gene or accession number submitted to design.

Note: the contents in this file are not viewable in the UCSC genome browser given that the RefSeq coordinates that it reports are not compatible with the browser.

Cancer50_Primer.bed

This file provides similar but more detailed information than the file Cancer50_Designed.bed . There are differences in the format of some columns and in the number of rows; the differences in format make this file compatible with the UCSC genome browser. This file presents two rows for each one of all of the targets submitted to design: one row for the forward primer and one row for the reverse primer. The start and end coordinates are for the position of the primer on the chromosome that is displayed in column 1. The second to last column reports the preferred TaqMan assay that can be used for verification. Also the gene symbol in the last column corresponds to the symbol submitted by the user (it might or might not be the HGNC symbol).

Cancer50_DataSheet.csv

This file contains one row for each of the RefSeq accession numbers of the RNA sequences that are covered by the designed primers. For each row there is extensive information such as the names submitted by the user, the corresponding HGNC approved symbol, the amplicon ID, the sequence of the forward and reverse primers, the start and end coordinates of the primers relative to the RefSeq sequence, the coordinates of the start and end of the amplicon and the start and end of the insert sequence relative to their position in the chromosome and the strand of the chromosome in which the sequence is located.

Summary: The Ion AmpliSeq™ RNA Cancer Panel is a screening tool designed against 50 oncogenes/tumor suppressor genes found in the COSMIC database. This panel has been developed as an RNA complement to the DNA focused Ion AmpliSeq™ Cancer Hotspot Panel v2. This panel contains 50 amplicons in 1 pool.